title: Pseudoislets Donor 21

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

data_processing:
The data was processed with the RNA-Seq Nextflow (v0.31.1) workflow, which can be found at https://github.com/nf-core/rnaseq.
Quality control was done with FASTQC (v0.11.7) and adapter trimming was performed by Trim Galore! (v0.5)
STAR (v2.6.1) was used for aligning the reads to the human reference genome GRCh38 Ensembl release 92
dupRadar (v1.10.0) was used for scanning RNA-Seq data for PCR clonal artifacts and the discovered duplicates were highlighted with Picard MarkDuplicates (v2.18.11)
Read counting on features (e.g. genes) was performed with featureCounts (v1.6.2)
For the differential expression analysis the raw read count table resulting from featureCounts was used and fed into the R package DESeq2 (v1.20)
Genome_build: GRCh38 Ensembl release 92
Supplementary_files_format_and_content: The tab-delimited text file that includes the raw read counts.

source_name: Human pancreatic pseudoislets

growth_protocol: Islets were cleaned immediately upon arrival by hand picking under a stereo dissecting microscope in Hank’s balanced salt solution supplemented by 0.25% bovine serum albumin (BSA). After an overnight culture in CMRL1066 medium containing (in mM): 5 glucose, 10 Hepes, 2 L-glutamine supplemented with 10% (v/v) fetal calf serum (FCS, Serva, Heidelberg, Germany) and antibiotics (100 U/ml), the islets were dissociated into single cells using trypsin (42.5 U/mL) in phosphate buffered saline containing 2 %(w/v) ethylenediamonetetraacetic acid (EDTA-PBS) and gentle shaking. Drops (20 µl of medium) containing 2000 cells were placed onto the top of a petri dish and cultured as hanging drops for 3 days. Medium was added to the bottom of the petri dishes to avoid drying out. The cells reaggregated within the hanging drop to form one pseudoislet. Each pseudoislet was then placed into a non-adhesive well of a 24-well-plate containing 0.5 ml medium and cultured for another 2 days.

extract_protocol:
Aliquots of cultured human islets and their respective pseudoislets were used for RNA extraction using NucleoSpin® RNA XS (Macherey-Nagel, Düren, Germany). RNA integrity (RIN≥9) was measured with Bioanalyzer 2100 (Agilent Technologies)
mRNA was isolated from 120 ng RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module. After fragmentation, the samples were subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra Directional RNA Library Prep II, NEB) and 75bp single read sequencing was performed on Illumina NextSeq500.

value: pseudoislets (reaggregated single-islet cells)

tag: individual

value: donor 21

value: 43 years old

tag: Sex

value: female


title: Pseudoislets Donor 22

status: Public on Nov 21 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: donor 22

tag: age

value: 53 years old


title: Run1 Wdr5 KO, T12hRescue-rep2

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

country: USA

institute: University of Michigan

description: Dox treated at T12h

data_processing:
All RNA-seq data were mapped to the mm10 genome for mouse using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Aligned reads were assembled using Cufflinks (v2.2.1) and assembled transcriptome catalog were used as input for Cuffdiff2 to determine expression levels (FPKM, Fragments Per Kilobase per Million mapped reads) and differential expression between conditions using default options. CummeRbund v2.1 (http://compbio.mit.edu/cummeRbund/) was then used to process, index, and visualize the output of the Cuffdiff2 analyses. Genes with q<0.01 and fold change (FC) >2 were considered to be differentially expressing genes.
Genome_build: mm10
Supplementary_files_format_and_content: expression Count and FPKM data

organism: Mus musculus

source_name: Embryoid bodies

growth_protocol: Rx:GFP mESCs were induced to differentiation with SFEBq method (5%KSR in GMEM media)

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.

treatment_protocol: 2% matrigel was added at EB day 1. Dox was added at T12h or T48h in hWDR5 inducible groups.

value: Embryoid bodies

tag: cell type

value: embryonic stem cell, Rx:GFP KI

tag: genotype

value: Wdr5 KO


title: Pseudoislets Donor 20

value: donor 20

value: 62 years old

value: male


title: Run1 Wdr5 KO, T12hRescue-rep1

description: Dox treated at T12h


title: Run2 Wdr5 KO-rep 1

description: No Dox


title: Run1 Wdr5 KO-rep 1

description: No Dox


title: HA(HA-hWDR5 T48h resuce)-ChIP-Seq

description: Dox inducible HA-hWDR5 at T48h

library_source: genomic

data_processing:
All ChIP-seq data were mapped to the mm10 genome for mouse by using Bowtie2 (v2-2.2.4), which is ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Then, we removed any duplicated reads for both pair-end and single-end data using SAMtools (v1.5)
Peaks of regulatory regions were called for each sample by using MACS (v 1.4.2)  from datasets of ChIP-Seq with parameters “-w -S -p 465 0.00001 -g mm”. The input signal was used as the control to call peaks for the ChIP-Seq dataset.  The heatmap plot of signals centered on peaks and gene promoters was implicated by deepTools2 (v2.5.0) . Peak annotation was performed by using HOMER (v4.9.1) with default parameters. Motif analysis on peak regions was performed with HOMER function  findMotifsGenome.pl with parameters “-size 50 -mask”.
The fold enrichment for visualization in IGV were calculated by bigwigCompare (Deeptools2 subcommand) based on the ratio of sigals (generated by MACS1.4) between the treatment and input control.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and peaks table

molecule: genomic DNA

source_name: embryoid bodies

extract_protocol:
ChIP experiments were performed using 15 µg anti-HA antibody for 3~4X107 cells according to standard protocols. Crosslinking of the cells was performed with 1% PFA for 10 minutesDisuccinimidyl glutarate crosslinker (COVAChem) at final concentration of 2 µM at room temperate for 30 min and 1% paraformaldehyde (Sigma) at room temperature at 10 min. ChIPed DNA was purified by Qiaquick PCR purification Kit (Qiagen).
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: 2% matrigel added at EB day 1. Dox were added at T12h or T48h in hWDR5 inducible groups.

value: embryoid bodies

value: Embryonic stem cell Rx:GFP KI

value: Wdr5 KO, hWDR5 T48h rescue


title: Run1 WT-rep1

description: untreated

value: WT


title: Pseudoislets Donor 19

value: donor 19

value: 48 years old


title: input (HA-hWDR5 T48h resuce)

description: Dox inducible HA-hWDR5 at T48h


title: Run1 WT-rep2

description: untreated


title: input (HA-hWDR5 T12h resuce)

description: Dox inducible HA-hWDR5 at T12h

value: Wdr5 KO, hWDR5 T12h rescue


title: Islets Donor 20

source_name: Human pancreatic islets

value: isolated islets


title: Islets Donor 21

value: donor 21

value: 43 years old

value: female


title: HA(HA-hWDR5 T12h resuce)-ChIP-Seq

description: Dox inducible HA-hWDR5 at T12h


title: Islets Donor 19_a


title: KO Cyto 1

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description:
KO.Cyto.R1.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files

molecule: polyA RNA

source_name: Cortex

extract_protocol:
PAR-CLIP m6A-seq was performed on cells isolated using scraping. m6A-seq and RNAseq were performed on RNA isolated as follows. The nuclear and cytoplasmic fractions of postnatal day 11 (P11) Fmr1KO wild type mouse cortices were isolated using the NE-PER kit (ThermoFisher #78835) following manufacturer’s instructions. The nuclear and cytoplasmic fractions of HEK293T cells were isolated using the following procedure: 3 million HEK293T cells were lysed on ice for 5 minutes using 60μl of NP40 lysis buffer (0.075% Nonidet P40, 10 mM Tris-HCl (pH 7.5), 150mM NaCl, 1:100 cOmplete EDTA-free protease inhibitor (Roche), 1:100 superase inhibitor (ThermoFisher AM2694). The cell lysate was layered over 150μl of chilled sucrose cushion (24% RNase-free sucrose in NP40 lysis buffer) and centrifuged at 4°C for 10 minutes at 15,000g. The supernatant was collected as the cytoplasmic fraction. The pellet was rinsed four times with PBS and collected as the nuclear fraction. The total, cytoplasmic, and nuclear fractions RNA were extracted using Trizol, mRNA was further purified using either one round of the mRNA DIRECT kit (ThermoFisher #61012) and one round of the RiboMinus Eukaryotic kit v2 (ThermoFisher #A15015), or two rounds of the mRNA DIRECT kit. RNA-seq library preparation was performed with TruSeq stranded mRNA sample preparation kit (Illumina).
Illumina TruSeq Stranded mRNA Library Prep Kit.

tag: strain/background

tag: genotype/variation

value: Fmr1 knockout

value: Cortex


title: Islets Donor 19_b


title: p53 and Wdr5 DKO; hWDR5iRescue T48h, EB6 (rep-2)

description: Dox inducible HA-hWDR5 at T48h

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality using Trim Galore! v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), powered by CutAdapt v1.8.1 (http://dx.doi.org/10.14806/ej.17.1.200) and FastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Paired-end reads were aligned using Bowtie2 (v2.2.9) mm10 and only reads mapped in proper pair were included by samtools (v1.4). Non-uniquely mapping reads and reads mapped to chrM, chrX or chrY were excluded.  Any candidate reads of PCR duplicates were removed by samtools (v1.4).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to centre the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v2.1.1.20160309) with a threshold of FDR-corrected P < 1 × 10−2 using the Benjamini–Hochberg procedure for multiple hypothesis correction.
As called peaks may be caused by noise in the assay and not reflect true chromatin accessibility, we calculated an irreproducible discovery rate (IDR) for all pairs of replicates across a cell type. The IDR is an estimate of the threshold where two ranked lists of results, in this case peak calls ranked by P value, no longer represent reproducible events. Using this measure, we excluded peaks that were not reproducible (IDR < 5 × 10−3) across at least one pair of replicates in each cell type.
The bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from filtered BAM files by using “bamCoverage” from deepTools with parameters “--outFileFormat bigwig --ignoreDuplicates --normalizeUsingRPKM --minMappingQuality 30  --binSize 50 --Offset 5 -1”.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

extract_protocol:
5x104 cells were used for transpoistion at 37C for 30 min using Illumina Nextera DNA Library Prep Kit.
Libraries were prepared with the Illumina Nextera DNA Library prep kit according to the manufacturer’s protocol.

treatment_protocol: 2% matrigel added at EB day 1. Dox was added at T12h or T48h in hWDR5 inducible groups.

value: p53 andWdr5 DKO, hWDR5 T48h rescue


title: TTC1240_ChIP_N106_SMARCB1_R377H_DPF2

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq and Mnase-seq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq, ATACseq and Mnase-seq data, output BAM files were converted into BigWig track files using BEDTools and UCSC utilities in order to display coverage throughout the genome (in RPM).
For the RNAseq data, tracks were generated using the deepTools v2.5.3 bamCoverage function.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of RNA or DNA fragments across the genome in reads per million.

source_name: tumor cell line

growth_protocol: TTC1240 and G401 cells were grown in DMEM (Gibco, 11960-44), supplemented with 10% FBS, 1X GlutaMAX (Gibco, 35050-061), 100 U/mL penicillin-streptomycin (Gibco, 15140-122), 1mM sodium pyruvate (Gibco, 11360-070), 1X MEM NEAA (Gibco, 11140-050), 10 mM HEPES, 1X 2-mercaptoethanol. The SMARCB1^K364del/+ iPSC cells were maintained in StemFlex Medium (Gibco) prior to differentiation. At Day (-2) of NGN2-mediated differentiation, the iPSCs were washed with 1X PBS (Gibco), and dissociated using Accutase (Innovative Cell Technologies).

extract_protocol:
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA). Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. All ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. RNA was collected in biological duplicate using the RNeasy Mini Kit (QIAGEN). All RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. ATAC-seq libraries were prepared in biological replicates using standard protocol (Buenrostro et al., Current Protocols (2013)) with 12 cycles of amplification. ATAC-seq samples were sequenced on Nex-seq 500 using 37 bp, 37 bp pair-end sequencing parameters.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). TTC1240 and G401 cells were lentivirally infected with either Empty vector, or one of four SMARCB1 variant constructs (full length, K364del, R377H, or delCC construct) for 48h and then selected with blasticidin for 5 days. Cells were harvested 7 days post-infection. Treatment: The SAH iPSC cell line underwent CRISPR/Cas9 mediated genome editing with a short-guide RNA (sgRNA) targeting exon 9 of the SMARCB1 gene and a single-stranded oligodeoxynucleotide (ssODN) donor strand encoding for the SMARCB1 K364del in-frame deletion. Cells were single cell sorted, genotyped and then confirmed via standard TA-cloning procedures to onbtain a SMARCB1+/+ WT control and K364del hetorzygous mutant (SMARCB1^K364del/+). The SMARCB1^K364del/+ iPSC cells were made into stable lines via lentiviral infection with either Empty vector or full-length SMARCB1 followed by blasticidin selection. Ngn2 differentiation of SAH cells: At Day (-2) cells were split and plated at 2K/well in geltrex coated plates. To induce NGN2-mediated differentiation, cells were infected with NGN2 lentiviral construct conjugated with EGFP and rTTA cassette on Day (-1). Media was changed periodically according to standard protocol.

tag: cell line

tag: ngs approach

value: ChIP-seq

tag: experimental condition

value: lentivirus:SMARCB1 R377H

tag: chip antibody


title: TTC1240_ChIP_N106_SMARCB1_K364del_DPF2

value: lentivirus:SMARCB1 K364del


title: Polysomal RNA Control replicate 1

city: Glasgow

first: Joseph

middle: Alexander

last: Waldron

address: Switchback road

country: United Kingdom

institute: Beatson Institute for Cancer Research

data_processing:
Reads were mapped to the MCF7 specific transcriptome using Bowtie (version 1.1.1), allowing for multi-mapping
expression levels were estimated at both the transcript and gene level using MMSEQ (version 1.0.10)
MMDIFF was used with the standard differential expression analysis to identify mRNAs which change in total RNA expression between control and hippuristanol treated conditions
MMDIFF was used with the difference of difference (DOD) analysis to identify mRNAs for which the log-fold change in expression between control and hippuristanol treated samples differed within the sub-polysomal and polysomal RNA
Genome_build: An MCF7 specific transcriptome was downloaded from http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/list.html
Supplementary_files_format_and_content: The DE files contain tab seperated values of the output from the differential expression analysis with MMDIFF. The feature_id contains the PacificBiosciences transcript or gene ID. This is followed by the bayes factor and posterior probability. alpha0 is the overall mean log(e) FPKM in control and hippuristanol treated samples when the expression in control and hippuristanol treated samples does not change, i.e. when the posterior probability is below the threshold set of 0.25, whereas alpha1 is the overal mean log(e) FPKM in control and hippuristanol treated samples for transcripts where the expression does change, i.e. when the posterior probability is above the threshold set of 0.25. eta1_0 is the log-fold change (hippuristanol - control) in expression. The final columns are the mean (mu) and standard deviation (sd) of the log(e) FPKM for each individual sample. TD = totals/DMSO(control) and TH = totals/hippuristanol. Each number represents the biological replicate.
Supplementary_files_format_and_content: The DOD files contain tab seperated values of the output from the difference of difference analysis with MMDIFF. The feature_id contains the PacificBiosciences transcript or gene ID. This is followed by the bayes factor and posterior probability. eta1_1 is the log-fold change (hippuristanol - control) in polysomal RNA expression, whereas eta1_2 is the log-fold change (hippuristanol - control) in sub-polysomal RNA expression . The final columns are the mean (mu) and standard deviation (sd) of the log(e) FPKM for each individual sample. PD = polysomal RNA/DMSO(control) and PH = polysomal RNA/hippuristanol, and SD = sub-polysomal RNA/DMSO(control) and SH = sub-polysomal RNA/hippuristanol. Each number represents the biological replicate.

source_name: Adherent breast cancer cell line

growth_protocol: MCF7 cells grown in DMEM, high glucose, GlutaMAX Supplement, pyruvate (ThermoFisher 31966-021), supplemented with 10% FCS

extract_protocol:
Cells were collected by gentle scraping and then lysed in 500 µl lysis buffer (15mM Tris-HCl pH 7.5, 300mM NaCl, 15mM MgCl2, 2mM DTT and 100 µg/ml cycloheximide, 1% Triton X, 1000U/ml SuperaseIn (AM2694)) for 1 min on ice. Lysate was centrifuged at 12,000g for 1 min at 4°C and the supernatant collected. 400 µl was loaded onto a 10-50% sucrose density gradient (15mM Tris-HCl pH 7.5, 300mM NaCl, 15mM MgCl2, 2mM DTT and 100 µg/ml cycloheximide) and centrifuged in a pre-cooled ultra-centrifuge with the SW40 Ti rotor at 38,000 rpm for 2h at 4°C. For total RNA samples, 50 µl lysate was added to 1ml TRIzol (ThermoFisher 15596026) and RNA was extracted as per manufacturer's instructions followed by isopropanol precipitation. Gradients were fractionated and 11 x 1ml fractions were collected and the RNA precipitated overnight at -20°C following the addition of 3ml guanidine HCl (7.7M) and 4ml 100% ethanol. Precipitated RNA was dissolved in 350 µl TE buffer and ethanol precipitated with 500mM ammonium acetate and 1 µl GlycoBlue. RNA was then dissolved in 30 µl Tris-HCl pH 7.5. Equal volumes of RNA from fractions 1-5 and 6-11 were each pooled to form the sub-polysomal and polysomal RNA respectively.
Illumina TrueSeq Stranded mRNA library preparation

treatment_protocol: Cells were treated for 1h with 150nM hippuristanol or an equal volume of DMSO (0.07%) by replenishment of the growth media. Following 1h incubation, cells were treated for 5 mins with 100  g/ml cycloheximide at 37°C before being washed with ice cold PBS containing 100 µg/ml cycloheximide.

tag: strain

tag: molecule type

value: polysomal

tag: treatment

value: control


title: TTC1240_ChIP_N106_SMARCB1_delCC_DPF2

value: lentivirus:SMARCB1 delCC (Y326*)


title: p53 and Wdr5 DKO; hWDR5iRescue T12h, EB6 (rep-2)

description: Dox inducible HA-hWDR5 at T12h

value: embryoid bodies

value: Embryonic stem cell Rx:GFP KI

value: p53 andWdr5 DKO, hWDR5 T12h rescue


title: TTC1240_ChIP_N106_SMARCB1_FL_DPF2

value: lentivirus:SMARCB1 FL


title: Wdr5 KO; hWDR5iRescue T12h, EB6 (rep-2)

description: Dox inducible HA-hWDR5 at T12h

value: Wdr5 KO, hWDR5 T12h rescue


title: Islets Donor 22

value: isolated islets

value: donor 22

value: 53 years old


title: TTC1240_ChIP_N106_SMARCB1_Empty_DPF2

value: lentivirus:SMARCB1 Empty


title: Run1 Wdr5 KO-rep 2

description: No Dox

value: Embryoid bodies

value: embryonic stem cell, Rx:GFP KI

value: Wdr5 KO


title: WT, EB6 (rep-2)

value: WT


title: G401_RNA_N106_SMARCB1_Empty_Rep1

value: tumor cell line

tag: lentivirus

value: SMARCB1 Empty


title: Wdr5 KO; hWDR5iRescue T48h, EB4 (rep-2)

description: Dox inducible HA-hWDR5 at T48h

value: Wdr5 KO, hWDR5 T48h rescue


title: G401_RNA_N106_SMARCB1_delCC_Rep2

value: SMARCB1 delCC (Y326*)


title: Wdr5 KO; hWDR5iRescue T48h, EB6 (rep-2)

description: Dox inducible HA-hWDR5 at T48h

value: embryoid bodies


title: G401_RNA_N106_SMARCB1_delCC_Rep1


title: Wdr5 KO; hWDR5iRescue T48h, EB4 (rep-1)

description: Dox inducible HA-hWDR5 at T48h

value: Embryonic stem cell Rx:GFP KI


title: WT, EB4 (rep-1)


title: WT, EB4 (rep-2)


title: G401_RNA_N106_SMARCB1_R377H_Rep2

value: SMARCB1 R377H


title: G401_RNA_N106_SMARCB1_R377H_Rep1


title: Wdr5 KO; hWDR5iRescue T12h, EB4 (rep-2)

description: Dox inducible HA-hWDR5 at T12h


title: Wdr5 KO; hWDR5iRescue T12h, EB4 (rep-1)

description: Dox inducible HA-hWDR5 at T12h


title: G401_RNA_N106_SMARCB1_Empty_Rep2


title: G401_RNA_N106_SMARCB1_K364del_Rep2

value: SMARCB1 K364del


title: G401_RNA_N106_SMARCB1_FL_Rep2

value: SMARCB1 FL


title: Wdr5 KO; hWDR5iRescue T12h, EB2 (rep-2)

description: Dox inducible HA-hWDR5 at T12h

value: Wdr5 KO, hWDR5 T12h rescue


title: Wdr5 KO, EB2 (rep-2)


title: G401_RNA_N106_SMARCB1_FL_Rep1


title: TTC1240_RNA_N106_SMARCB1_delCC_Rep2


title: G401_RNA_N106_SMARCB1_K364del_Rep1


title: Wdr5 KO; hWDR5iRescue T12h, EB2 (rep-1)

description: Dox inducible HA-hWDR5 at T12h


title: Wdr5 KO, EB2 (rep-1)


title: TTC1240_RNA_N106_SMARCB1_R377H_Rep2


title: TTC1240_RNA_N106_SMARCB1_delCC_Rep1


title: WT, EB2 (rep-1)


title: WT, EB2 (rep-2)


title: TTC1240_RNA_N106_SMARCB1_R377H_Rep1


title: TTC1240_RNA_N106_SMARCB1_K364del_Rep2


title: TTC1240_RNA_N106_SMARCB1_FL_Rep2


title: TTC1240_RNA_N106_Empty_Rep2

value: empty


title: TTC1240_RNA_N106_SMARCB1_FL_Rep1


title: TTC1240_ATAC_N106_SMARCB1_delNterm_Day9

value: SMARCB1 delN terminus


title: TTC1240_RNA_N106_Empty_Rep1


title: A549 cells, Input

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
The reads were mapped to the CRISPR SAM sgRNA library and raw reads for each sgRNA were counted using the MAGeCK pipeline.
sgRNA enrichment was determined using the MAGeCK-MLE analysis pipeline.
Supplementary_files_format_and_content: bulkSAMseq_ISREifnaA549_mapped.csv reports raw counts for each sgRNA

source_name: A549 human lung epithelial cell line

growth_protocol: A549 cells maintained throughout in complete growth media.

extract_protocol:
Cells were sorted via flow cytometry, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers. PCR amplified libraries were generated with independent barcodes to allow multiplexing.

treatment_protocol: Cells were transduced with the SAM sgRNA library, incubated for 48 h, then treated with interferon alpha for 6 h before collection.

value: A549 human lung epithelial cell line

tag: transduction

value: untransduced

value: not sorted


title: TTC1240_ATAC_N106_SMARCB1_delCC_Rep2


title: TTC1240_ATAC_N106_SMARCB1_delCterm_Day9

value: SMARCB1 delC terminus


title: adjacent 2

city: Jinan

first: Lu

last: Yu

state: Shandong

address: No.44-1 Wenhua Road West

department: Department of Implantology

country: China

institute: School and Hospital of Stomatology, Shandong University

data_processing:
Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAILING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25)
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression.
The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(fold change)| > 1 using the DEGseq software. Finally, a hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads and RPKM values for each samples

source_name: ventrum of tongue

extract_protocol:
the tissues were removed from patients and total RNA was extracted from tissues using the Trizol (invitrogen) reagent
Fragmented RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA). The libraries were paired-end sequenced (PE150, Sequencing reads were 150 bp) at Guangzhou RiboBio Co., Ltd. (Guangzhou, China)using IlluminaHiSeq 3000 platform.

value: ventrum of tongue

tag: disease

value: normal


title: adjacent 3

source_name: gingiva

value: gingiva


title: tumor 3

tag: pt

tag: pn

tag: histologic grade

value: Oral squamous cell carcinoma


title: tumor 1

source_name: root of tongue

tag: age

tag: tissue

value: root of tongue


title: A549 cells, SAMTrans2

value: SAM sgRNA library transduced


title: tumor 2


title: adjacent 1


title: A549 cells, SAMTrans1


title: TTC1240_ATAC_N106_SMARCB1_delCC_Rep1

tag: cell type

value: tumor cell line

value: SMARCB1 delCC (Y326*)


title: TTC1240_ATAC_N106_SMARCB1_R377H_Rep2

value: SMARCB1 R377H


title: TTC1240_RNA_N106_SMARCB1_K364del_Rep1

value: SMARCB1 K364del


title: A549 cells, SAM2

value: interferon treated and sorted


title: A549 cells, SAM1


title: BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 19

city: Valencia

first: Susana

last: Rodríguez Navarro

state: Valencia

address: Jaume Roig, 11

department: Patología y Terapia Molecular y Celular

country: Spain

institute: Instituto de Biomedicina de Valencia

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

data_processing:
Both RNAseq and ChIPseq data were obtained after Illumina sequencing and fastq files were obtained from Macrogen server
RNAseq: Raw sequencing data quality was checked by fastqc and good overall quality was observed in all cases
RNAseq: Reads mapped to the yeast saccer3 genome with Tophat21 and genes were cuantified with HTSEQ2 intersection-option
ChIPseq: Raw sequencing data quality was checked by fastqc and good overall quality was observed in all cases
ChIPseq: Illumina adapters trimming was needed and it was performed using cutadapt
ChIPseq: Reads were mapped to the yeast saccer3 genome with Bowtie2
ChIPseq: Regions with high coverage were defined using MACS2 (peak calling step)
ChIPseq: All the regions found in H4K12ac samples were merged into a single .bed file using bedtools (H4K12peaks.bed)
ChIPseq: The .bed file was used as an annotation file to compute the counts across regions using HTSEQ2 intersection-option
Genome_build: saccer3
Supplementary_files_format_and_content: RNAseq: we provide the count matrix in which expression values for each Saccharomyces cerevisiae gene were quantified in each sample through HTSEQ2
Supplementary_files_format_and_content: ChIPseq: we provide the count matrix in which the coverage values for each region (previously defined) were quantified in each sample.  H4K12peaks.bed with regions merged.

organism: Saccharomyces cerevisiae

source_name: BY4741 wt yeast cells

growth_protocol: For all samples, yeast cells were growth until exponential phase (O.D.600 = 0.7) in rich medium (YPD). Each culture is then split in three flasks at equal amounts. One flask is maintained at 30ºC and its labeled at time point 0. The other two flasks are incubated at 39°C for 20 minutes and 120 minutes, respectively by adding preheated media to reach 39ºC instantly. These two last flasks capture the heat-shock response while the 30°C flask serves as a control of non-stress conditions.

extract_protocol:
For RNAseq samples, a 10 mL aliquote is collected from each culture, washed twice with pure water and celular pellet was then frozen in liquid nitrogen. Total RNA was extracted with hot acid phenol protocol.
For ChIPseq samples, a crosslinking reaction was performed with 1% formaldehyde for 15 minutes and the reaction was then stopped with 125 mM glycine for then washing three times the pellet with TBS buffer and frozen in liquid nitrogen. ChIP experiment was performed with 1 microL per sample of H4 (ab10158) or H4K12ac (39165 Active Motif) antibodies bound to magnetic beads and incubated for 2 hours before IP. It followed the genomic DNA extraction with phenol protocol.
For RNA: TruSeq Stranded Total RNA Sample Prep . For ChIPseq: ChIPseq specific library
TruSeq for RNAseq and ChIPseq library for ChIPseq

tag: genotype

value: wt

tag: growth condition

value: Histone H4K12ac antibody catalog No 39165 (Active Motif)

tag: biological replicate


title: BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 21

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

source_name: BY4741 mip6D yeast cells


title: BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 23

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 24

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: TTC1240_ATAC_N106_SMARCB1_K364del_Rep2

tag: cell line


title: BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 16

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

tag: chip antibody


title: TTC1240_ATAC_N106_SMARCB1_R377H_Rep1


title: Leaves, HL+HS-3

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: Highlight + Heat stress

data_processing:
Illumina's two-channel SBS sequencing
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file includes mean normalized counts for each sample

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

growth_protocol: Arabidopsis thaliana Col-0 plants were grown in peat pellets (jiffy) at 23°C under long day growth conditions (12-hour light from 7 AM to 7 PM/12-hour dark from 7 PM to 7 AM; 50 µmol m-2 s-1).

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions and purified using NucleoSpin RNA Clean-up kit (Macherey-Nagel).
RNA-Seq libraries (TruSeq) using a poly A enrichment method

treatment_protocol: 30-day-old Arabidopsis thaliana Col-0  plants were subjected to high light (600 µmol m-2 s-1), heat stress (42°C) and the combination of high light and heat stress during 7h.

tag: ecotype

tag: stress

value: Highlight + Heat stress

tag: repeat

value: wild type

value: leaves


title: Leaves, CT-3

description: Control

value: Control


title: BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 14

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

tag: strain


title: BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 15

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: TTC1240_ATAC_N106_SMARCB1_FL_Rep2

tag: lentivirus

value: SMARCB1 FL


title: TTC1240_ATAC_N106_SMARCB1_K364del_Rep1


title: BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 13

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: Leaves, HL-3

description: Highlight stress

value: Highlight stress


title: Leaves, HS-3

description: Heat stress

value: Heat stress


title: BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 17

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: ChIP-Seq: CTCF

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

data_processing:
Basecalling software: Illumina RTA
bowtie 1.0.0 for ChIP-Seq readmapping, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto cells were synchronized in G1

extract_protocol:
ChIP-Seq: Cells were cross-linked and scraped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
ChIP libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue type

value: cervical carcinoma

value: HeLa Kyoto

tag: RNAi

value: CTCF


title: BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 10

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: TTC1240_ATAC_N106_SMARCB1_FL_Day9

value: tumor cell line


title: Leaves, HL+HS-2

description: Highlight + Heat stress


title: TTC1240_ATAC_N106_Empty_Rep2

value: empty


title: Leaves, HS-2

description: Heat stress


title: BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 8

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 wt yeast cells, 30ºC , H4K12ac ChIPseq 11

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: Leaves, HL-2

description: Highlight stress


title: ChIP-Seq: STAG2

value: GFP


title: TTC1240_ATAC_N106_Empty_Day9


title: ChIP-Seq: STAG1


title: BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 7

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: ChIP-Seq: SMC3


title: TTC1240_ChIP_SMARCB1_delCC_H3K27Ac

value: SMARCB1 delCC (Y326*)


title: Leaves, CT-2

description: Control


title: PUS10_PAR_CLIP_Rep2

city: Beijing

first: Jinghui

last: Song

address: 5 Yiheyuan Road, Haidian District

institute: Peking university

description:
Total RNA
processed data file:
PAR_CLIP_sites.txt
Antibody: Mouse monoclonal anti-Flag M2 Magnetic Beads (Sigma-Aldrich, M8823)

data_processing:
Basecalls performed using Illumina CASAVA.
For reads cleanning, adaptor were trimmed and low quality reads were filtered with Trim_galore software (version: 0.3.3).
Cleaned reads were mapped to reference genome (hg19 and genomic tRNA database [GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/)]) using TopHat version 2.1.0 (rRNA(-) nuclear RNA-seq and polyA RNA-seq) and Bowtie version 1.2.2 (PAR-CLIP-seq and DM-Ψ-seq).
Abundance measurements were performed by Cufflinks version 2.2.1 (polyA RNA-seq) and Htseq-count version 0.9.1 (rRNA(-) nuclear RNA-seq). Peak-calling of PAR-CLIP were performed by PARalyzer version 1.5. Site-calling of DM-Ψ-seq were performed by custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values, peak calling and site calling for each group of samples.

growth_protocol: HEK293T cells were maintained at 37 °C in DMEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
For rRNA(-) nuclear RNA-seq, cell fractionation was performed, and the resulting RNA was subjected to two rounds of rRNA removal using RiboMinus™ Eukaryote Kit for RNA-Seq .For polyA RNA-seq, total RNA was isolated from cell lines with Trizol (invitrogen) according to the manufacturer’s instructions. Two rounds of poly-A selection were performed using Dynabeads™ Oligo(dT)25 (Invitrogen) to obtain mRNA. For PAR-CLIP-seq, five 15 cm dishes of HEK293T cells were transfected with flag-tagged PUS10 plasmid at 80% confluency. After 6 h, the media was changed and 200 μM 4SU was added. After additional 18 h, the cells were washed once with 10 ml ice-cold PBS for each plate. Then, the plates were kept on ice, and the UV crosslink was carried out twice by 150 mJ/cm2 at 365 nm. After immunoprecipitation,  the final recovered RNA sample was further cleaned by RNA Clean & Concentrator (Zymo Research). For DM-Ψ-seq, small RNA (<200 nt) was isolated and purified from cell culture using miRNeasy Mini Kit, RNeasy MinElute Cleanup Kit and RNase-free DNase Set (Qiagen) according to the manufacturer’s instructions.
The rRNA(-) nuclear RNA and poly-A RNA were used to construct RNA-seq library under the instruction of NEBNext® Ultra™ RNA Library Prep Kit for Illumina. For PAR-CLIP-seq, the RNA samples were used to construct library under the instruction of NEBNext® Multiplex Small RNA Library Prep Set for Illumina. For DM-Ψ-seq,  the library construction was performed according to the eCLIP library construction protocol with several modifications.

treatment_protocol: For cell passage, cells were first washed with PBS. Trypsin was added to the dishes, which were then incubate at 37 °C for 2-5 min, and FBS containing medium was used to inactive trypsin. After collected by centrifuge at 1000 g for 3 min, cells were counted and split for different purposes. Generation of PUS10 knockout HEK293T cells was achieved by using CRISPR/Cas9 technology.


title: BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 6

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: Leaves, HL+HS-1

description: Highlight + Heat stress


title: TTC1240_ATAC_N106_SMARCB1_FL_Rep1


title: BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 5

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 4

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: KO_BEU_Rep1

description:
small RNA
processed data file:
DM_psiU_seq_KO_sites.txt
Libraries were sequenced with paired-end strategy but due to the particularity of our library construction (a random barcode of 10 nt were included in our 3' end cDNA adapter, which cannot be precisely located in Read 1), data of Read 1 were discarded and only the data of Read 2 were used in our analysis. Only Read 2 was submitted.

data_processing:
Library strategy: DM-psiU-seq
Basecalls performed using Illumina CASAVA.
For reads cleanning, adaptor were trimmed and low quality reads were filtered with Trim_galore software (version: 0.3.3).
Cleaned reads were mapped to reference genome (hg19 and genomic tRNA database [GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/)]) using TopHat version 2.1.0 (rRNA(-) nuclear RNA-seq and polyA RNA-seq) and Bowtie version 1.2.2 (PAR-CLIP-seq and DM-Ψ-seq).
Abundance measurements were performed by Cufflinks version 2.2.1 (polyA RNA-seq) and Htseq-count version 0.9.1 (rRNA(-) nuclear RNA-seq). Peak-calling of PAR-CLIP were performed by PARalyzer version 1.5. Site-calling of DM-Ψ-seq were performed by custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values, peak calling and site calling for each group of samples.


title: TTC1240_ChIP_SMARCB1_K364del_H3K27Ac

value: SMARCB1 K364del


title: PUS10_PAR_CLIP_Rep1


title: Leaves, HS-1

description: Heat stress


title: TTC1240_ChIP_SMARCB1_Empty_H3K27Ac


title: TTC1240_ChIP_SMARCB1_R377H_H3K27Ac

value: SMARCB1 R377H


title: Leaves, HL-1

description: Highlight stress


title: BY4741 wt yeast cells, 39ºC 20', H4K12ac ChIPseq 3

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: wt

value: Histone H4K12ac antibody catalog No 39165 (Active Motif)


title: TTC1240_ChIP_SMARCB1_FL_H3K27Ac


title: BY4741 wt yeast cells, 30ºC , H4K12ac ChIPseq 2

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: TTC1240_ChIP_N106_SMARCB1_delCC_V5_SMARCB1

value: SMARCB1/BAF47 (Cell Signaling Tech., 91735S (D8M1X), lot:1)


title: TTC1240_ChIP_N106_SMARCB1_delCC_SMARCC1

value: SMARCC1/BAF155 (Cell Signaling Tech., 11956S (D7F8S), lot:2)


title: TTC1240_ChIP_N106_SMARCB1_delCC_SMARCA4

value: BRG1/SMARCA4 (Abcam, ab110641 [EPNCIR111A], lot:GR150844-37)


title: TTC1240_ChIP_N106_SMARCB1_R377H_V5_SMARCB1


title: BY4741 wt yeast cells, 30ºC , H4K12ac ChIPseq 1

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 23

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: Anti-H4 ab10158 (Abcam)


title: BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 21

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 22

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: Leaves, CT-1

description: Control

value: Control

value: wild type

value: leaves


title: BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 24

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: T47D_Hi-C_Serum_rep5

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: Hi-C(PE)

data_processing:
We processed Hi-C data by using an in-house pipeline based on TADbit and OneD algorithms (Serra et al., 2017; Vidal et al., 2018). First, the quality of the reads was checked with FastQC to discard problematic samples and detect systematic artifacts. Trimmomatic (Bolger et al., 2014) with the recommended parameters for PE reads was used to remove adaptor sequences and poor-quality reads (ILLUMINACLIP: TruSeq3-PE.fa:2:30:12:1:true; LEADING:3; TRAILING:3; MAXINFO:targetLength:0.999; and MINLEN:36).
For mapping, a fragment-based strategy implemented in TADbit was used, which was similar to previously published protocols (Ay et al., 2015). Briefly, each side of the sequenced read was mapped in full length to GRCh38. After this step, if a read was not uniquely mapped, we assumed that the read was chimeric, owing to ligation of several DNA fragments. We next searched for ligation sites, discarding those reads in which no ligation site was found. The remaining reads were split as often as ligation sites were found. Individual split read fragments were then mapped independently. These steps were repeated for each read in the input FASTQ files. Multiple fragments from a single uniquely mapped read resulted in a number of contacts identical to the number of possible pairs between the fragments. For example, if a single read was mapped through three fragments, a total of three contacts (all-versus-all) was represented in the final contact matrix. We used the TADbit filtering module to remove non-informative contacts and to create contact matrices. The different categories of filtered reads applied were:
1. Self-circle: reads coming from a single restriction enzyme (RE) fragment and pointing to the outside.
2. Dangling end: reads coming from a single RE fragment and pointing to the inside.
3. Error: reads coming from a single RE fragment and pointing in the same direction.
4. Extra dangling end: reads coming from different RE fragments but that were sufficiently close and point to the inside; the distance threshold used was left to 500 bp (default), which was between percentiles 95 and 99 of average fragment lengths.
5. Duplicated: the combination of the start positions and directions of the reads was repeated, thus suggesting a PCR artifact; this filter removed only extra copies of the original pair.
6. Random breaks: the start position of one of the reads was too far from RE cutting site, possibly because of non-canonical enzymatic activity or random physical breaks; the threshold was set to 750 bp (default), >percentile 99.9.
From the resulting contact matrices, low-quality bins (those presenting low contact numbers) were removed, as implemented in TADbit’s ‘filter columns’ routine. A single round of ICE normalization (Imakaev et al., 2012), also known as ‘vanilla’ normalization (Rao et al., 2014), was performed. That is, each cell in the Hi-C matrix was divided by the product of the interactions in its columns and the interactions in its row. Finally, all matrices were corrected to achieve an average content of one interaction per cell.
Identification of sub-nuclear compartments and TADs
To segment the genome into A/B compartments, normalized Hi-C matrices at 100-kb resolution were corrected for decay as previously described, by grouping diagonals when the signal-to-noise ratio was below 0.05 (Rao et al., 2014). Corrected matrices were then split into chromosomal matrices and transformed into correlation matrices by using the Pearson product-moment correlation.
Normalized contacts matrices at 20-kb resolution were used to define TADs, and for visualization purposes, through a previously described method with default parameters (Crane et al., 2015; Giorgetti et al., 2016). First, for each bin, an insulation index was obtained on the basis of the number of contacts between bins on each side of a given bin. Differences in the insulation index between both sides of the bin were computed, and borders were called, searching for minima within the insulation index. The insulation score of each border was determined as previously described (Crane et al., 2015), by using the difference in the delta vector between the local maximum to the left and the local minimum to the right of the boundary bin. This procedure resulted in a set of borders for each time point and replicate. To obtain a set of consensus borders along the time course, we proceeded in two steps: (i) merging borders of replicates and overlapping merged borders (that is, for each pair of replicates, we expanded the borders one bin on each side and kept only those borders present in both replicates as merged borders) and (ii) further expanding two extra bins (100 kb) on each side and determining the overlap to obtain a consensus set of borders common to any pair of time points.
Intra-TAD contacts
Using Hi-C matrices at 5 kb resolution, we focused on TADs containing TFIIIC. We labeled each bin according to TFIIIC and CTCF occupancy as well as gene promoter annotation. Genes were classified according to RNA-seq results as "changed" or "unchanged". The former set was further divided into "up" and "down". We marked as "others" bins not overlapping any of the corresponding categories.
Then, we gathered the non-observed contacts between the different types of bins within their TAD and computed expected contacts frequencies based on the genomic distance that separate each pair (the expected distance decay was calculated excluding entries outside TADs). We used the log2 of the ratio on observed over expected as a contact score. We summarized the results via linear mixed-effects models fitted using lme4 (Ziyatdinov et al., 2018). We considered TADs as a random effect and the aforementioned bin categories (and their interactions) as fixed effects.
We fitted linear mixed models using lmer function of lme4 R package (and computed the posterior probabilities using sim function of arm R package for the corresponding interaction terms
Genome_build: hg38

extract_protocol: In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate.

tag: media

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

tag: serum

value: serum-starved


title: T47D_Hi-C_noSerum_siCTRL_rep1

description: Hi-C(PE)


title: T47D_Hi-C_noSerum_siCTRL_rep2

description: Hi-C(PE)


title: T47D_Hi-C_noSerum_siGTF3C5_rep1

description: Hi-C(PE)


title: TTC1240_ChIP_N106_SMARCB1_delCC_INPUT

value: tumor cell line


title: Old.3

type: RNA

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Hybridized on Illumina Mouse-6 v2 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Arrays were quantile normalized and the data filtered to remove non-informative probes that were expressed at background levels in the majority of the samples or had a maximum fold change below 1.2 between any two samples.  A total of 25,988 probes were retained for further analysis.  Replicates available for 2 samples were averaged prior to statistical analysis.

label: biotin

source_name: B cells, old mouse

label_protocol: Biotin labeled cDNA at 750ng obtained from ASCs of young and aged mice

growth_protocol: Mice were obtained from Charles River labs and housed in the Wistar Institute’s animal facility. Young mice were 6-8 weeks of age, and aged mice were >17 months of age

extract_protocol: Total RNA and small RNA were isolated from sorted ASCs using the modified protocol of Ambion RNAqueous -Micro kit (cat #AM1931) to recover the small RNAs.

treatment_protocol: Mice were euthanized by CO2 asphyxiation, and samples were collected. Bone marrow samples were isolated from the bones of the hind legs of each mouse.Bone marrow resident cells were stained for extracellular markers. Cells were then sorted on a FACS ARIA fluorescent cell sorter for ASCs.

tag: condition

value: Old

tag: replicate

value: B cells

tag: age

value: >17 months


title: Old.2

tag: cell type


title: Old.4


title: T47D_Hi-C_noSerum_rep5

description: Hi-C(PE)


title: Old.5


title: TTC1240_ChIP_N106_SMARCB1_R377H_SMARCA4


title: Old.6


title: Old.1


title: BY4741 wt yeast cells, 30ºC , H4 ChIPseq 20

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

tag: genotype

tag: growth condition


title: BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 19

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

tag: biological replicate


title: T47D_Hi-C_Serum_rep3

description: Hi-C(PE)

tag: cell line

value: RPMI supplemented with 10% FBS

value: non-serum starved


title: T47D_Hi-C_noSerum_rep6

description: Hi-C(PE)


title: BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 18

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: wt

tag: chip antibody


title: TTC1240_ChIP_N106_SMARCB1_R377H_INPUT

value: SMARCB1 R377H


title: TTC1240_ChIP_N106_SMARCB1_K364del_V5_SMARCB1

value: SMARCB1 K364del

value: SMARCB1/BAF47 (Cell Signaling Tech., 91735S (D8M1X), lot:1)


title: T47D_Hi-C_noSerum_rep4

description: Hi-C(PE)


title: T47D_Hi-C_Serum_rep2

description: Hi-C(PE)


title: Young.9

source_name: B cells, young mouse

value: Young

value: 6-8 weeks


title: BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 17

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: Anti-H4 ab10158 (Abcam)


title: TTC1240_ChIP_N106_SMARCB1_K364del_SMARCC1

value: SMARCC1/BAF155 (Cell Signaling Tech., 11956S (D7F8S), lot:2)


title: BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 16

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: T47D_Hi-C_noSerum_rep3

description: Hi-C(PE)


title: TTC1240_ChIP_N106_SMARCB1_K364del_SMARCA4

value: BRG1/SMARCA4 (Abcam, ab110641 [EPNCIR111A], lot:GR150844-37)


title: Young.7


title: T47D_Hi-C_noSerum_rep2

description: Hi-C(PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h


title: TTC1240_ChIP_N106_SMARCB1_K364del_INPUT


title: Young.8


title: BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 14

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: Patient D endometrium

type: genomic

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

description: methylation profiling using bisulfite converted

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing: Data was analysed using R version 3.4.1 (2017-06-30). Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘Champ’ R package (v. 2.12.0), with quality control options set as default. The quality control step retained 745259 probes, which were used for further analysis. Probes overlapped with SNP (78353) and with a detection pvalue < 0.01 (9769), beadcount <3 in at least 5% of samples in one or more samples (12568) were eliminated. X or Y chromosomes probes (17283), non-cg probes (2812), and probes aligning to multiple locations (47) and unannotated probes were also removed from analysis. No background correction was carried out. SWAN normalisation was applied, with the ‘method’ option set to “minfi”. The SWAN normalized samples were assigned with respective genome coordinates based on probe name and manifest file (Illumina Inc., USA).

label: Cy5 and Cy3

source_name: genomic DNA from endometrium tissue of Patient D

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from control placenta, biparental mole and sporadic mole by using the QIAamp DNA FFPE Tissue Kit (Qiagen).

value: Endometrium tissue

tag: disease state

value: Normal


title: TTC1240_ChIP_N106_SMARCB1_FL_SMARCC1

value: tumor cell line

value: SMARCB1 FL


title: TTC1240_ChIP_N106_SMARCB1_FL_V5_SMARCB1


title: BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 12

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: T47D_Hi-C_Serum_rep1

description: Hi-C(PE)


title: BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 13

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: T47D_mRNA_sGTF3C5_noSerum_expB_rep2

description: RNA-seq pair end (PE)

data_processing:
RNA-seq analysis.  (https://docs.google.com/document/d/1yRZevDdjxkEmda9WF5-qoaRjIROZmicndPl3xetFftY/edit?usp=sharing)
RNA-seq analysis. Differential expression (www.dropbox.com/s/026pc48kfuqr88g/RNA_analysis_deseq.2.R?dl=0)
Genome_build: hg38

extract_protocol:
RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads.
To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads.

value: serum-starved


title: TTC1240_ChIP_N106_SMARCB1_FL_SMARCA4


title: Sporadic Mole (AnCHM)

source_name: genomic DNA from molar conceptus of AnCHM mother

value: Molar conceptus

value: Affected (Androgenetic Complete Hydatidiform Mole)


title: TTC1240_ChIP_N106_SMARCB1_FL_INPUT


title: BY4741 wt yeast cells, 30ºC , H4 ChIPseq 11

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: wt


title: Young.4.2

value: B cells


title: Young.6


title: Endometrium of AnCHM mother

source_name: genomic DNA from endometrium tissue of AnCHM mother


title: Young.5


title: BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 15

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: KHDC3L Mole (BiCHM)

source_name: genomic DNA from molar conceptus of Patient D

value: Affected (Biparental Complete Hydatidiform Mole)


title: Control Placenta 02

source_name: genomic DNA from control placenta

value: Placenta


title: Young.4.1

value: Young


title: Young.3.2

value: 6-8 weeks


title: Young.2


title: BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 10

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: Anti-H4 ab10158 (Abcam)


title: TTC1240_ChIP_N106_Empty_V5_SMARCB1

value: empty

value: SMARCB1/BAF47 (Cell Signaling Tech., 91735S (D8M1X), lot:1)


title: T47D_mRNA_Serum_expB_rep2

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% FBS

value: non-serum starved


title: TTC1240_ChIP_N106_Empty_SMARCA4

value: BRG1/SMARCA4 (Abcam, ab110641 [EPNCIR111A], lot:GR150844-37)


title: T47D_mRNA_Serum_expA_rep1

description: RNA-seq pair end (PE)


title: BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 8

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 9

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: Control Placenta 01

value: Normal


title: T47D_total_RNA_noSerum_rep1

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h


title: TTC1240_ChIP_N106_Empty_INPUT

value: tumor cell line


title: Young.3.1


title: T47D_total_RNA_Serum_rep1

description: RNA-seq pair end (PE)


title: Young.1


title: BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 7

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: T47D_mRNA_noSerum_expB_rep2

description: RNA-seq pair end (PE)

value: serum-starved


title: BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 6

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 5

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: T98G_TFIIIC_serum_recovery

description: ChIP-seq single end (SE)

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). P-values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment.

value: DMEM with 10% FBS, followed by 48h starvation, then 10%FBS is added back for 30'

value: reserum

tag: chip-antibody

value: in house anti-GTF3C2 rabbit polyclonal


title: T47D_CTCF_NoSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: rabbit polyclonal antibody anti-CTCF Millipore 07-729


title: SAH_iPSC_RNA_SMARCB1_WT_Day8_Rep1

source_name: SAH

value: induced pluripotent stem cell line

value: SAH

value: wild type

tag: time

value: day 8


title: SAH_iPSC_RNA_SMARCB1_WT_Day8_Rep2


title: TTC1240_ChIP_N106_Empty_SMARCC1

tag: lentivirus

value: empty

value: SMARCC1/BAF155 (Cell Signaling Tech., 11956S (D7F8S), lot:2)


title: SAH_iPSC_RNA_SMARCB1_WT_Day4_Rep2

value: day 4


title: SAH_iPSC_RNA_SMARCB1_WT_Day4_Rep1


title: T47D_CTCF_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% FBS

value: non-serum starved


title: T47D_H3K18ac_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house rabbit polyclonal antibody anti-H3K18ac


title: BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 3

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

tag: strain

value: wt

value: Anti-H4 ab10158 (Abcam)


title: SAH_iPSC_RNA_SMARCB1_WT_Day2_Rep1

value: day 2


title: LNCap +R 388+KD

city: Atlanta

first: Jindan

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 18

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: ATCC

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS or 5% charcoal-stripped serum, 1% penicillin-streptomycin.

extract_protocol: Total RNA were extracted using Trizol according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: Cells were hormone starved with RPMI supplemented with 5% charcoal-stripped serm for 3 days, treat with or without 1nM R1881 for 24h.

value: LNCaP

tag: knockdown rna

tag: transfected with

tag: treatment


title: SAH_iPSC_RNA_SMARCB1_WT_Day2_Rep2


title: IMR90_serum_input

description: ChIP-seq single end (SE)

tag: media

value: EMEM with 10% FBS

tag: serum


title: IMR90_TFIIIC_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house anti-GTF3C2 rabbit polyclonal


title: LNCap +R FENG+KD

description: SAMPLE 16

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: FENG+KD

value: FENG


title: BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 4

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: LNCap +R 266+KD

description: SAMPLE 17

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.


title: SAH_iPSC_RNA_SMARCB1_WT_Day0_Rep2

value: induced pluripotent stem cell line

value: SAH

value: day 0


title: IMR90_TFIIIC_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: DMEM with 10% FBS, followed by 48h starvation

value: serum-starved


title: TTC1240_ChIP_N106_SMARCB1_R377H_SMARCC1

value: tumor cell line

value: SMARCB1 R377H

value: SMARCC1/BAF155 (Cell Signaling Tech., 11956S (D7F8S), lot:2)


title: BY4741 mip6D yeast cells, 30ºC , RNAseq 23

description: CountMatrixRNAseq.xlsx


title: LNCap +R 253+KD

description: SAMPLE 15


title: LNCap +R WT+KD

description: SAMPLE 12

value: WT+KD

value: WT


title: BY4741 mip6D yeast cells, 39ºC 120', RNAseq 24

description: CountMatrixRNAseq.xlsx


title: LNCap +R 87+KD

description: SAMPLE 13


title: LNCap +R 226+KD

description: SAMPLE 14


title: BY4741 wt yeast cells, 30ºC , H4 ChIPseq 2

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed

value: wt

value: Anti-H4 ab10158 (Abcam)


title: T98G_noSerum_input

description: ChIP-seq single end (SE)


title: BY4741 mip6D yeast cells, 39ºC 20', RNAseq 22

description: CountMatrixRNAseq.xlsx


title: BY4741 wt yeast cells, 30ºC , H4 ChIPseq 1

description:
CountMatrixChIPseq.xlsx
H4K12peaks.bed


title: LNCap -R 388+KD

description: SAMPLE 9

value: LNCaP

value: ethanol


title: T98G_TFIIIC_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house anti-GTF3C2 rabbit polyclonal


title: LNCap +R GFP+KD

description: SAMPLE 11

value: GFP+KD

value: GFP


title: T98G_serum_input

description: ChIP-seq single end (SE)

value: DMEM with 10% FBS

value: non-serum starved


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day8_Rep1

value: induced pluripotent stem cell line

value: SAH

value: day 8


title: BY4741 mip6D yeast cells, 39ºC 20', RNAseq 21

description: CountMatrixRNAseq.xlsx


title: LNCap -R 266+KD

description: SAMPLE 8


title: SAH_iPSC_RNA_SMARCB1_WT_Day0_Rep1

value: wild type

value: day 0


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day8_Rep2


title: BY4741 wt yeast cells, 30ºC , RNAseq 20

description: CountMatrixRNAseq.xlsx


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day4_Rep2

value: day 4


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day4_Rep1


title: T98G_TFIIIC_Serum_ChIP-seq

description: ChIP-seq single end (SE)


title: BY4741 wt yeast cells, 39ºC 20', RNAseq 18

description: CountMatrixRNAseq.xlsx


title: BY4741 wt yeast cells, 39ºC 120', RNAseq 19

description: CountMatrixRNAseq.xlsx


title: BY4741 wt yeast cells, 39ºC 120', RNAseq 17

description: CountMatrixRNAseq.xlsx


title: BY4741 mip6D yeast cells, 30ºC , RNAseq 16

description: CountMatrixRNAseq.xlsx


title: T47D_noSerum_input

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

value: serum-starved


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day2_Rep2

value: day 2


title: LNCap -R 226+KD

description: SAMPLE 5


title: LNCap -R FENG+KD

description: SAMPLE 7

value: FENG+KD

value: FENG


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day2_Rep1


title: T47D_BDP1_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house anti-BDP1 rabbit polyclonal


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day0_Rep2


title: SAH_iPSC_RNA_SMARCB1_K364delHet_Day0_Rep1


title: T47D_POL3_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% FBS

value: in house anti-POL3 rabbit polyclonal


title: BY4741 mip6D yeast cells, 39ºC 20', RNAseq 15

description: CountMatrixRNAseq.xlsx


title: BY4741 mip6D yeast cells, 30ºC , RNAseq 14

description: CountMatrixRNAseq.xlsx


title: SAH_iPSC_ChIP_WT_Day0_SUZ12

value: SUZ12 (Cell Signaling Tech., 3737S, lot:6)


title: BY4741 mip6D yeast cells, 39ºC 120', RNAseq 13

description: CountMatrixRNAseq.xlsx


title: LNCap -R WT+KD

description: SAMPLE 3

value: LNCaP

value: WT+KD

value: WT

value: ethanol


title: AD-CAB 2025

city: Waurn Ponds

first: Nima

last: Kamal

state: VIC

address: 75 Pigdons Rd

department: School of Medicine

country: Australia

institute: Deakin University

data_processing:
Samples performed using NovaSeq 600 Sequencing system
FASTQ format converted to .CSV using Linux, WinSCP and PuTTy software
Data with no reads were filtered using edgeR in R
Data were trimmed using edgeR in R with specifications of false discovery rate (FDR) values < 0.05
Pathways were found using PANTHER software
Genome_build: Ensembl genome browser 97
Supplementary_files_format_and_content: Data were generated using edgeR in R; that included fold change (FD), counts per million (CPM), p value and FDR value

source_name: Shoulder Capsule

growth_protocol: Adhesive capsulitis protocol

extract_protocol:
Total RNA extraction using Qiagen RNA
NuGen Universal Plus mRNA-Seq according to manufacturer' protocols (15 cycles of PCR). NovaSeq on 300 cycle flowcell generating 2x151 read length

treatment_protocol: RNAlater

tag: age

tag: Sex

value: Male


title: AD-CAB 2026

value: Female


title: LNCap -R GFP+pGIPZ

description: SAMPLE 1

tag: genotype

value: GFP+pGIPZ

value: pGIPZ control

value: GFP


title: LNCap -R GFP+KD

description: SAMPLE 2

value: GFP+KD


title: LNCap -R 87+KD

description: SAMPLE 4


title: T47D_POL3_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

value: serum-starved


title: AD-CAB 2024


title: BY4741 wt yeast cells, 39ºC 20', RNAseq 12

description: CountMatrixRNAseq.xlsx

value: wt

tag: growth condition


title: iNPC_P25_2_2

city: Shanghai

first: Ting

last: Zhang

address: 100 Haining Road

department: Department of Ophthalmology

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were mapped to the hg19 version of human genome using TopHat2 version 2.0.4 program
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks version 2.0.2 software
Genes with the FPKM>1.0 in at least one sample across all samples were retained for further analysis and the expression levels were transformed to log-space by using the log2 (FPKM+1).
Genome_build: hg19
Supplementary_files_format_and_content: .txt file includes FPKM values for each gene in each Sample

source_name: Induced neural progenitor cells

growth_protocol: PB MNCs were isolated from 4-8 ml peripheral blood using Ficoll-Paque Premium (Sigma) by density gradient centrifugation. The MNCs were then culture for 8 to 12 days in MNC medium,  which favors the expansion of erythroblast but do not support lymphocytes growth. human iNPCs were maintained on Matrigel-coated dish in NSC medium containing 20 ng/ml EGF and 20 ng/ml FGF2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA was reversed transcribed by SuperScript II reverse transcriptase (Invitrogen). The double-stranded cDNA was amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and purified using 1: 0.75 ratio of AMPure XP beads (Bechman Coulter).
Amplified cDNA (~5 ng) was then used to construct Illumina sequencing libraries using Illumina’s Nextera DNA sample preparation kit following the manufacturer’s instructions.

tag: cell type

value: neural progenitor cells

tag: passages

tag: donor age

tag: gender

value: male


title: T47D_Serum_input

description: ChIP-seq single end (SE)

tag: cell line

value: RPMI supplemented with 10% FBS

value: non-serum starved

tag: chip-antibody


title: iNPC_P25_2_1


title: BY4741 wt yeast cells, 30ºC , RNAseq 11

description: CountMatrixRNAseq.xlsx

tag: biological replicate


title: BY4741 wt yeast cells, 39ºC 120', RNAseq 10

description: CountMatrixRNAseq.xlsx

tag: strain


title: LNCap -R 253+KD

description: SAMPLE 6

value: LNCaP

tag: knockdown rna


title: SAH_iPSC_ChIP_WT_Day0_SMARCB1

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq and Mnase-seq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq, ATACseq and Mnase-seq data, output BAM files were converted into BigWig track files using BEDTools and UCSC utilities in order to display coverage throughout the genome (in RPM).
For the RNAseq data, tracks were generated using the deepTools v2.5.3 bamCoverage function.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of RNA or DNA fragments across the genome in reads per million.

value: induced pluripotent stem cell line

value: SAH

value: wild type

tag: chip antibody

value: SMARCB1/BAF47 (Cell Signaling Tech., 91735S (D8M1X), lot:1)

tag: time

value: day 0


title: AD-CAB 2023

value: Female


title: SAH_iPSC_ChIP_WT_Day0_SMARCA4

value: BRG1/SMARCA4 (Abcam, ab110641 [EPNCIR111A], lot:GR3208604-7)


title: iNPC_P25_1_2


title: T47D_mRNA_siCTRL_noSerum_expB_rep2

description: RNA-seq pair end (PE)

tag: media


title: AD-CAB 2021

value: Male


title: SAH_iPSC_ChIP_WT_Day0_RNAPolII


title: T47D_BDP1_Serum_ChIP-seq

description: ChIP-seq single end (SE)

tag: serum

value: in house anti-BDP1 rabbit polyclonal


title: BY4741 wt yeast cells, 39ºC 20', RNAseq 9

description: CountMatrixRNAseq.xlsx


title: iNPC_P25_1_1


title: SAH_iPSC_ChIP_WT_Day0_SMARCC1

value: SMARCC1/BAF155 (Cell Signaling Tech., 11956S (D7F8S), lot:2)


title: AD-CAB 2020

tag: age


title: AD-CAB 2022

tag: Sex


title: iNPC_P15_2_2


title: BY4741 mip6D yeast cells, 39ºC 20', RNAseq 8

description: CountMatrixRNAseq.xlsx

tag: genotype


title: AD-CAB 2019


title: AD-CAB 2018


title: iNPC_P15_1_2


title: AD-CAB 2017


title: SAH_iPSC_ChIP_WT_Day0_H3K27ac


title: SAH_iPSC_ChIP_K364delHet_Day0_SUZ12

value: SUZ12 (Cell Signaling Tech., 3737S, lot:6)


title: SAH_iPSC_ChIP_K364delHet_Day0_SMARCC1


title: iNPC_P15_1_1


title: PB MNC_2

source_name: Peripheral blood mononuclear cells

value: peripheral blood mononnuclear cells


title: BY4741 wt yeast cells, 39ºC 120', RNAseq 4

description: CountMatrixRNAseq.xlsx

value: wt

tag: growth condition


title: AD-CAB 2015


title: PB MNC_1

tag: cell type

value: male


title: SAH_iPSC_ChIP_WT_Day0_Input


title: SAH_iPSC_ChIP_K364delHet_Day0_SMARCB1


title: AD-CAB 2014


title: BY4741 wt yeast cells, 39ºC 20', RNAseq 3

description: CountMatrixRNAseq.xlsx


title: SAH_iPSC_ChIP_WT_Day0_H3K27me3


title: iNPC_P15_2_1

value: neural progenitor cells

tag: passages


title: SAH_iPSC_ChIP_K364delHet_Day0_SMARCA4


title: AD-CAB 2013


title: BY4741 wt yeast cells, 30ºC , RNAseq 2

description: CountMatrixRNAseq.xlsx


title: HeLa H5N1 replicate 2

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the human GRCh38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing FPKM quantification for all samples

source_name: HeLa H5N1

extract_protocol:
After 9 hours, cell extracts were collected with Trizol and total RNA was extracted using RNeasy Mini Kit (Qiagen).
Strand-specific polyA-selected sequencing libraries were produced according to standard Illumina protocols.

treatment_protocol: Cells were mock-infected or infected with A/WSN33 or H5N1-HALo at a MOI of 3. After 1 hour, cells were washed and then incubated with medium at 37 °C.

value: HeLa

tag: infection

value: H5N1 HALo


title: HeLa H5N1 replicate 1


title: BY4741 mip6D yeast cells, 39ºC 120', RNAseq 6

description: CountMatrixRNAseq.xlsx


title: AD-CAB 2012


title: HeLa WSN replicate 2

source_name: HeLa WSN

value: H1N1 WSN


title: m287_ChIP-seq_LNCap -R 388+pGIPZ shFoxA1

description: LNCap -R AR 388+pGIPZ shFoxA1

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: Prostate cancer cell line

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS or  5% charcoal-stripped serum

extract_protocol: Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated by using the indicated antibody.  DNA was then uncrosslinked from protein, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer. Libraries were prepared according to Illumina's instructions.

treatment_protocol: LNCaP cells were co-infected with FoxA1 knockdown and FoxA1 WT or muatnts lentivirus and puro selected for 4-5 days, hormone starvation for 3 days, treat with or without 10nM R1881 for 16h before fixation by 1% paraformaldehyde.

value: LNCaP

value: 388+pGIPZ shFoxA1

tag: transfected with

tag: treatment

value: Ethanol

tag: antibody

value: AR

tag: vendor

value: Santa Cruz

tag: catalog number

tag: lot/batch number


title: HeLa WSN replicate 1

tag: cell line


title: AD-CAB 2011


title: m284_ChIP-seq_LNCap -R 266+pGIPZ shFoxA1

description: LNCap -R AR 266+pGIPZ shFoxA1

value: 266+pGIPZ shFoxA1

tag: knockdown rna


title: BY4741 mip6D yeast cells, 30ºC , RNAseq 5

description: CountMatrixRNAseq.xlsx

source_name: BY4741 mip6D yeast cells

tag: strain

tag: biological replicate


title: AD-CAB 2010

tag: age

value: Male


title: HeLa mock replicate 2

source_name: HeLa mock

value: mock


title: SAH_iPSC_ChIP_K364delHet_Day0_H3K27ac

extract_protocol:
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA). Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. All ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. RNA was collected in biological duplicate using the RNeasy Mini Kit (QIAGEN). All RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. ATAC-seq libraries were prepared in biological replicates using standard protocol (Buenrostro et al., Current Protocols (2013)) with 12 cycles of amplification. ATAC-seq samples were sequenced on Nex-seq 500 using 37 bp, 37 bp pair-end sequencing parameters.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

value: induced pluripotent stem cell line

value: SAH

tag: chip antibody

tag: time

value: day 0


title: AD-CAB 2009

tag: Sex


title: HeLa mock replicate 1


title: LNCap +R GFP+pGIPZ

description: SAMPLE 10

tag: genotype

value: GFP+pGIPZ

value: pGIPZ control

value: GFP


title: SAH_iPSC_ATAC_SMARCB1_WT_Day0_Rep2

tag: cell type

value: wild type


title: BY4741 mip6D yeast cells, 39ºC 120', RNAseq 7

description: CountMatrixRNAseq.xlsx

tag: growth condition


title: SAH_iPSC_ATAC_SMARCB1_WT_Day0_Rep1


title: m316_ChIP-seq_LNCap -R 253+pGIPZ shFoxA1

description: LNCap -R AR 253+pGIPZ shFoxA1

value: 253+pGIPZ shFoxA1

tag: transfected with


title: A549 mock replicate 2

source_name: A549 mock

tag: infection


title: AD-CAB 2016


title: m283_ChIP-seq_LNCap -R 226+pGIPZ shFoxA1

description: LNCap -R AR 226+pGIPZ shFoxA1

value: 226+pGIPZ shFoxA1

tag: treatment

tag: antibody


title: AD-CAB 2007


title: BY4741 wt yeast cells, 30ºC , RNAseq 1

description: CountMatrixRNAseq.xlsx

source_name: BY4741 wt yeast cells

value: wt


title: AD-CAB 2008


title: SAH_iPSC_ATAC_SMARCB1_K364delHet_Day0_Rep2


title: A549 mock replicate 1


title: m282_ChIP-seq_LNCap -R 87+pGIPZ shFoxA1

description: LNCap -R AR 87+pGIPZ shFoxA1

value: LNCaP

value: 87+pGIPZ shFoxA1

tag: vendor

tag: catalog number


title: SAH_iPSC_ChIP_K364delHet_Day0_H3K27me3

tag: cell line


title: m317_ChIP-seq_LNCap -R FENG+pGIPZ shFoxA1

description: LNCap -R AR FENG+pGIPZ shFoxA1

value: FENG+pGIPZ shFoxA1

tag: knockdown rna

value: FENG

value: Ethanol

value: AR

tag: lot/batch number


title: SAH_iPSC_ATAC_SMARCB1_K364delHet_Day0_Rep1


title: SAH_iPSC_ChIP_K364delHet_Day0_RNAPollII


title: 293T cells, Control +IFN C

data_processing:
The reads were mapped to the human transcriptome (hg19) using STAR and the samples were run on Basespace (Illumina).
Mapped reads were normalized and averaged; fold change then calculated by comparing the interferon alpha treated samples to untreated samples.
Genome_build: hg19
Supplementary_files_format_and_content: bulkRNAseq_ETV7ifna293T_mapped.csv reports raw counts

source_name: 293T human kidney cell line

growth_protocol: 293T cells maintained throughout in complete growth media.

extract_protocol:
At 9 h post interferon treatment, cells were lysed and total RNA collected using the Monarch Total RNA Miniprep Kit (NEB).
mRNA was prepped for sequencing using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II RNA Library Prep Kit (NEB #E7770), and NEBNext Multiplex Oligos for Illumina (NEB #E7335, #E7500).

treatment_protocol: Cells were transfected with plasmids, incubated for 36 h, then treated or not with interferon alpha for 9 h before collection.

value: 293T human kidney cell line

tag: transfection

value: mCherry-expressing plasmid

value: interferon alpha


title: PBAT_KHDC3L_embryo_day6

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina NextSEq 500 platform using the default RTA analysis software.
Raw sequence reads had the first 9 base pairs clipped off the 5' end to remove the 9N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.4, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 9 --clip_r2 9). For the PBAT sample, trimming was carried out in paired-end mode, and remaining sequences were then aligned to the human genome (build GRCh38) in paired-end mode using Bismark (v0.19.1; parameters: --pbat). Single-cell data was trimmed and aligned in the same manner but in single-end mode (v0.19.1; parameters: --non_directional). Methylation calls were extracted after duplicate sequences had been excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: embryo day 6

extract_protocol:
DNA was extracted from single embryo by lysing cells in 0.5% SDS in EB buffer with proteinase K for 1 hour at 37 degrees.
The PBAT protocol was also employed to analyse DNA methylation of the embryo, using a slightly adapted method for bulk samples as described in [Hanna et al. 2018].

treatment_protocol: Mature oocytes were obtained after ovarian stimulation using a standard GnRH antagonist protocol.  Out of 9 oocytes, 7 were collected for subsequent single-cell BS-seq analysis. Intracytoplasmic sperm injection (ICSI) was performed followed by 6 days embryo culture with the 2 remaining oocytes, resulting in one embryo, which was collected for whole-embryo BS-seq analysis.

tag: tissue

value: embryo day 6

tag: age

value: 27 years

value: KHDC3L mutant

tag: protocols

value: PBAT


title: SAH_iPSC_ChIP_K364delHet_Day0_Input

value: induced pluripotent stem cell line

value: SAH

tag: chip antibody

tag: time

value: day 0


title: m281_ChIP-seq_LNCap -R WT+pGIPZ shFoxA1

description: LNCap -R AR WT+pGIPZ shFoxA1

tag: genotype

value: WT+pGIPZ shFoxA1

value: WT

value: Santa Cruz


title: AD-CAB 2005

tag: Sex

value: Male


title: 293T cells, Control +IFN B


title: m279_ChIP-seq_LNCap -R GFP+pGIPZ

description: LNCap -R AR GFP+pGIPZ

value: LNCaP

value: GFP+pGIPZ

value: pGIPZ

tag: transfected with

value: GFP


title: AD-CAB 2003


title: 293T cells, Control -IFN C

value: 293T human kidney cell line

value: mCherry-expressing plasmid

value: no treatment


title: m298_ChIP-seq_LNCap +R 388+pGIPZ shFoxA1

description: LNCap +R AR 388+pGIPZ shFoxA1

value: 388+pGIPZ shFoxA1

value: AR


title: m297_ChIP-seq_LNCap +R 266+pGIPZ shFoxA1

description: LNCap +R AR 266+pGIPZ shFoxA1

value: 266+pGIPZ shFoxA1


title: AD-CAB 2001


title: 293T cells, Control -IFN A


title: 293T cells, Control -IFN B


title: scBS_KHDC3L_MII_2

source_name: oocyte

extract_protocol:
DNA was extracted from single oocytes by lysing cells in RLT+ Buffer (Qiagen).
DNA methylation of single oocytes was assessed using whole-genome bisulphite sequencing according to the post-bisulphite adaptor tagging (PBAT) protocol as described by [Smallwood 2014; Angermueller et al. 2016].

value: oocyte

value: 27 years

value: KHDC3L mutant

value: scBS


title: m322_ChIP-seq_LNCap +R FENG+pGIPZ shFoxA1

description: LNCap +R AR FENG+pGIPZ shFoxA1

value: FENG+pGIPZ shFoxA1

value: FENG


title: scBS_KHDC3L_MII_1


title: AD-CAB 2006

value: Female


title: AD-CAB 2002


title: scBS_KHDC3L_MII_3


title: m280_ChIP-seq_LNCap -R GFP+pGIPZ shFoxA1

description: LNCap -R AR GFP+pGIPZ shFoxA1

value: LNCaP

value: GFP+pGIPZ shFoxA1

value: Ethanol

value: Santa Cruz


title: AD-CAB 1026


title: m321_ChIP-seq_LNCap +R 253+pGIPZ shFoxA1

description: LNCap +R AR 253+pGIPZ shFoxA1

value: 253+pGIPZ shFoxA1


title: 293T cells, ETV7 +IFN C

value: 293T human kidney cell line

value: ETV7-expressing plasmid

value: interferon alpha


title: AD-CAB 1023


title: 293T cells, ETV7 +IFN B


title: T47D_mRNA_sGTF3C5_noSerum_expA_rep1

description: RNA-seq pair end (PE)

tag: media

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

tag: serum

value: serum-starved


title: scBS_KHDC3L_MII_6

value: oocyte


title: AD-CAB 2004

value: Male


title: AD-CAB 1022


title: scBS_KHDC3L_MII_5

value: 27 years

value: KHDC3L mutant


title: m290_ChIP-seq_LNCap +R 87+pGIPZ shFoxA1

description: LNCap +R AR 87+pGIPZ shFoxA1

value: 87+pGIPZ shFoxA1

tag: treatment

tag: antibody

value: AR


title: 293T cells, Control +IFN A

value: mCherry-expressing plasmid


title: T47D_mRNA_siCTRL_noSerum_expA_rep1

description: RNA-seq pair end (PE)


title: 293T cells, ETV7 +IFN A


title: m291_ChIP-seq_LNCap +R 226+pGIPZ shFoxA1

description: LNCap +R AR 226+pGIPZ shFoxA1

value: LNCaP

value: 226+pGIPZ shFoxA1

tag: vendor

tag: catalog number


title: m320_ChIP-seq_LNCap +R WT+pGIPZ shFoxA1

description: LNCap +R AR WT+pGIPZ shFoxA1

tag: cell line

value: WT+pGIPZ shFoxA1

tag: knockdown rna

value: WT


title: T47D_mRNA_siGTF3C5_noSerum_24h_serum_readdition_rep2

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, followed by re-addition of 10% charcoal-treated (CT) FBS after the indicated time

value: serum-starved + charcoal-treated (CT) 24h


title: AD-CAB 1020


title: T47D_mRNA_noSerum_expA_rep1

description: RNA-seq pair end (PE)


title: 293T cells, ETV7 -IFN B

value: 293T human kidney cell line

tag: transfection

value: ETV7-expressing plasmid

value: no treatment


title: 293T cells, ETV7 -IFN A


title: m319_ChIP-seq_LNCap +R GFP+pGIPZ shFoxA1

description: LNCap +R AR GFP+pGIPZ shFoxA1

value: GFP+pGIPZ shFoxA1

value: GFP

value: Santa Cruz

tag: lot/batch number


title: AD-CAB 1019

tag: age

value: Male


title: T47D_mRNA_siCTRL_noSerum_24h_serum_readdition_rep2

description: RNA-seq pair end (PE)


title: AD-CAB 1018

value: Female


title: T47D_mRNA_siCTRL_noSerum_24h_serum_readdition_rep1

description: RNA-seq pair end (PE)

value: serum-starved + charcoal-treated (CT) 12h


title: m277_ChIP-seq_LNCap -R 266+pGIPZ shFoxA1

description: LNCap -R HA 266+pGIPZ shFoxA1

value: 266+pGIPZ shFoxA1

value: Ethanol

value: HA

value: Abcam


title: m278_ChIP-seq_LNCap -R 388+pGIPZ shFoxA1

description: LNCap -R HA 388+pGIPZ shFoxA1

value: LNCaP

value: 388+pGIPZ shFoxA1


title: RNA-seq of control HEK239T cells, bioreplicate 2

city: Chicago

first: zhike

address: 5801 South Ellis Avenue

institute: University of Chicago

description:
HEK.siCtrl.repl.2
RPKM_HEK293T_siFMR1.xlsx

data_processing:
The adapters and low quality bases were removed by using cutadapt(v1.1.5)
The fastq files were aligned to the reference genome(hg38) using Tophat(v2.1.1)
Stringtie(v1.3.3b) was used to caculate the RPKM for each gene.
Genome_build: hg38
Supplementary_files_format_and_content: RPKM

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in high-glucose DMEM medium with 10% FBS and 1% Pen/Strep and passaged at 1:10 ratio every three days

extract_protocol:
RNA extraction was performed using Trizol and Zymo Direct-zol miniprep kit
After two rounds of polyA selection, RNA-seq libraries were constructed using illumina Truseq stranded mRNA kit

treatment_protocol: HEK293T cells were treated with FMR1 siRNA or control siRNA in parallel for 48 hours before being collected in Trizol

tag: sirnas

value: siControl


title: T47D_mRNA_siGTF3C5_noSerum_12h_serum_readdition_rep2

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, followed by re-addition of 10% charcoal-treated (CT) FBS after the indicated time


title: RNA-seq of HEK239T deficent of FMRP, bioreplicate 2

description:
HEK.siFMR1.rep.2
RPKM_HEK293T_siFMR1.xlsx


title: RNA-seq of HEK239T deficent of FMRP, bioreplicate 1

description:
HEK.siFMR1.rep.1
RPKM_HEK293T_siFMR1.xlsx


title: AD-CAB 1016


title: AD-CAB 1021


title: m307_ChIP-seq_LNCap -R FENG+pGIPZ shFoxA1

description: LNCap -R HA FENG+pGIPZ shFoxA1

value: FENG+pGIPZ shFoxA1

value: FENG


title: AD-CAB 1014


title: AD-CAB 1017


title: RNA-seq of control HEK239T cells, bioreplicate 1

description:
HEK.siCtrl.repl.1
RPKM_HEK293T_siFMR1.xlsx


title: T47D_mRNA_siGTF3C5_noSerum_12h_serum_readdition_rep1

description: RNA-seq pair end (PE)


title: T47D_mRNA_siCTRL_noSerum_12h_serum_readdition_rep1

description: RNA-seq pair end (PE)


title: AD-CAB 1012


title: m318_ChIP-seq_LNCap +R GFP+pGIPZ

description: LNCap +R AR GFP+pGIPZ

value: GFP+pGIPZ

value: pGIPZ

value: AR


title: HEK R2 IP

description:
HEK.Total.R2.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: HEK m6Aseq.xlsx

data_processing:
Library strategy: m6A-seq
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files

extract_protocol:
PAR-CLIP m6A-seq was performed on cells isolated using scraping. m6A-seq and RNAseq were performed on RNA isolated as follows. The nuclear and cytoplasmic fractions of postnatal day 11 (P11) Fmr1KO wild type mouse cortices were isolated using the NE-PER kit (ThermoFisher #78835) following manufacturer’s instructions. The nuclear and cytoplasmic fractions of HEK293T cells were isolated using the following procedure: 3 million HEK293T cells were lysed on ice for 5 minutes using 60μl of NP40 lysis buffer (0.075% Nonidet P40, 10 mM Tris-HCl (pH 7.5), 150mM NaCl, 1:100 cOmplete EDTA-free protease inhibitor (Roche), 1:100 superase inhibitor (ThermoFisher AM2694). The cell lysate was layered over 150μl of chilled sucrose cushion (24% RNase-free sucrose in NP40 lysis buffer) and centrifuged at 4°C for 10 minutes at 15,000g. The supernatant was collected as the cytoplasmic fraction. The pellet was rinsed four times with PBS and collected as the nuclear fraction. The total, cytoplasmic, and nuclear fractions RNA were extracted using Trizol, mRNA was further purified using either one round of the mRNA DIRECT kit (ThermoFisher #61012) and one round of the RiboMinus Eukaryotic kit v2 (ThermoFisher #A15015), or two rounds of the mRNA DIRECT kit. RNA-seq library preparation was performed with TruSeq stranded mRNA sample preparation kit (Illumina).
Illumina TruSeq Stranded mRNA Library Prep Kit.

tag: genotype/variation

value: Wild-type


title: AD-CAB 1011


title: m275_ChIP-seq_LNCap -R 87+pGIPZ shFoxA1

description: LNCap -R HA 87+pGIPZ shFoxA1

value: 87+pGIPZ shFoxA1


title: T47D_mRNA_siGTF3C5_noSerum_3h_serum_readdition_rep2

description: RNA-seq pair end (PE)

value: serum-starved + charcoal-treated (CT) 3h


title: HEK R1 IP

description:
HEK.Total.R1.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: HEK m6Aseq.xlsx


title: AD-CAB 1010

value: Female


title: T47D_mRNA_siGTF3C5_noSerum_3h_serum_readdition_rep1

description: RNA-seq pair end (PE)


title: m276_ChIP-seq_LNCap -R 226+pGIPZ shFoxA1

description: LNCap -R HA 226+pGIPZ shFoxA1

value: 226+pGIPZ shFoxA1